The complete chloroplast genome of Philodendron hederaceum (Jacq.) Schott 1829 (Alismatales: Araceae)

Abstract Philodendron hederaceum (Jacq.) Schott 1829, a species of the Araceae family, is a foliage plant of ornamental value. The complete chloroplast genome sequence of Philodendron hederaceum was obtained by the de novo assembly of NovaSeq 6000 (Illumina Co., San Diego, CA) paired-end short reads and Oxford Nanopore long reads. The complete chloroplast genome of P. hederaceum was 168,609 bp in length, with a large single-copy (LSC) region of 94,393 bp, a small single-copy (SSC) region of 25,774 bp, and a pair of identical inverted repeat regions (IRs) of 24,221 bp. The genome contained a total of 129 genes, including 85 protein-coding genes, 36 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. The phylogenetic analysis of P. hederaceum with 19 related species and two outgroup species revealed the closest taxonomical relationship with Philodendron lanceolatum in the Araceae family.


Introduction
Philodendron is the second-largest genus belonging to the Araceae, the tropical monocot family characterized by diverse morphology and a wide geographic distribution in the Neotropics (Loss-Oliveira et al. 2016;Goncalves and Mayo 2000).
The Philodendron genus comprises 482 species (Boyce and Croat 2018).Its geographic distribution, spanning from Northern Mexico to Southern Uruguay (Mayo et al. 1997), contributes to the formation of rainforests in the Amazon and South America.The species belonging to the Philodendron genus are mainly distributed in Brazil, where 168 species were reported (Coelho et al. 2016).While the inflorescence morphology of Philodendron is generally conserved, the leaf morphology and habitats of Philodendron exhibit a wide range of diversity (Coelho 2000;Coelho et al. 2016).Philodendron species are classified into three subgenera based on floral and vegetative morphology (Mayo 1991;Croat 1997): the subgenus Meconostigma (Schott) Engl.(Gonc ¸alves and Salviani 2002), the subgenus Pteromischum (Schott) Mayo (Coelho 2000), and the subgenus Philodendron (Coelho 2000).
P. hederaceum (Jacq.)Schott 1829, also known as the heart-leaf philodendron, is native to Central America and the Caribbean.It is characterized by bright glossy heart-shaped dark green leaves and is used as an ornamental plant.P. hederaceum is an evergreen climber that reaches a height of 3-6 m and occasionally produces yellow-green and white flowers (Goncalves and Mayo 2000), adding to its ornamental appeal.This study presents the complete chloroplast genome of Philodendron hederaceum, aiming to explore further phylogenetic relationships within the Philodendron genus.

Materials and methods
The P. hederaceum plants were initially collected in Ciudad de Panam� a, Panama (9 � 01 0 40 00 N 79 � 33 0 50 00 W), following the local regulations and with the necessary permissions from local authorities.Subsequently, the collected P. hederaceum plants were propagated and are currently maintained in the greenhouse at the Natural Science Research Institute, Sahmyook University, Seoul, South Korea (Figure 1).The voucher specimen with the collection number SYFS101 has been deposited at the Natural Science Research Institute, Sahmyook University, Seoul, South Korea (https://www.syu.ac.kr/natural-science-institute/, contact person: Jae Hwan Lee, dlwoghks1236@naver.com).This institute is affiliated with the National Agrobiodiversity Center at Rural Development Administration, Jeonju, South Korea, and serves as the institute for agricultural genetic resources.
The genomic DNA was extracted from the leaf tissues of P. hederaceum using a modified CTAB (cetrimonium bromide)-based protocol.Subsequently, DNA quantitation and integrity were validated using Nanodrop (Thermo Scientific Inc., Waltham, MA) and agarose gel electrophoresis.The construction of the Illumina paired-end (PE) genomic library was performed using the NEXTflex V R Rapid DNA sequencing kit (Bioo Scientific, Austin, TX), following the manufacturer's protocol.The chloroplast genome of P. hederaceum was sequenced using NovaSeq6000 (Illumina Inc., San Diego, CA), and subsequently, low-quality and adaptor sequences were removed with Trimmomatic (Bolger et al. 2014).To circularize the chloroplast genome, additional long-read sequences were generated using Oxford Nanopore Promethion24 (Oxford Nanopore Technologies Inc., Oxford, UK), following the manufacturer's recommendations for constructing the long-read sequencing library.
To complete the chloroplast genome assembly, we constructed a hybrid assembly using both Illumina and Nanopore sequences with an Organelle PBA assembler (Soorni et al. 2017).Subsequently, error correction of the final contig was carried out using Illumina reads with NextPolish (ver.1.3.0,https://github.com/Nextomics/NextPolish).The gene prediction for the assembled chloroplast genome was executed using GeSeq (Tillich et al. 2017) with subsequent manual correction.Following annotation, the entire chloroplast genome sequence of P. hederaceum was submitted to GenBank under the accession number OM937109.
To investigate the phylogenetic position of P. hederaceum, we obtained the complete chloroplast genome sequences of 14 related species in Araceae from GenBank, along with two outgroup species (Sagittaria lichuanensis and Thalassia hemprichii).The sequences were aligned using ClustalW (ver.2.1) (Larkin et al. 2007).Subsequently, a phylogenetic tree was constructed through the maximum-likelihood (ML) method with 1000 bootstraps, utilizing MEGA 10.2.5 (Kumar et al. 2016).

Discussion and conclusions
The complete chloroplast genome sequence of Philodendron hederaceum is 168,609 bp in size and contains 94,393 bp of LSC, 25,774 bp of SSC, and 24,221 bp of two IR regions.It harbors 85 protein-coding genes, 36 tRNAs, and eight ribosomal RNAs (rRNAs).Phylogenetic analysis involving P. hederaceum and 19 complete chloroplast genomes of the registered species in the Araceae family revealed Philodendron lanceolatum as its closest relative.Notably, there are differences in chloroplast gene content between P. hederaceum and its closely related species, P. lanceolatum.P. lanceolatum exhibits the absence of three photosystem-related genes, an additional copy of tRNA genes, and ycf ORFs compared to P. lanceolatum (Henriquez et al. 2020).This insight into the chloroplast   14 psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbT, rps14, rps15, rps16, rps18, rps19, rps2, rps3, rps4, rps7 (x2) genome of P. hederaceum is anticipated to facilitate further investigations into phylogenetic relationships and the evolution of chloroplast genes in Philodendron.

Figure 1 .
Figure 1.Photograph of Philodendron hederaceum (Jacq.)Schott 1829 (these photographs were taken by Jae Hwan Lee).The foliage of P. hederaceum exhibits heart-shape and glossy texture on cascading stems.Upper surface of leaves has medium to dark green color, while lower surface has medium green color.The primary lateral veins have 2-6 per side, and emerge from the midvein at an angle of 35 � to 55 � .(A) Plants of P. hederaceum, (B) the leaf of P. hederaceum, and (C) the stem of P. hederaceum.

Figure 2 .
Figure 2. Chloroplast genome map of Philodendron hederaceum.Genes inside the circle are transcribed in a counterclockwise direction, and genes outside the circle are transcribed in a clockwise direction.The color of each gene represents its function.LSC, SSC, IRa, and IRb regions are indicated in this map.